Bioinformatic Tools in CRISPR/Cas Platform

Malaria parasites, Plasmodium can infect a wide range ofhosts including humans and rodents. There are two copies ofmitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise ofpresented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series ofpublicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localizedandcontain both a nuclear localization signal (NLS) anda Leucine-rich nuclear export signal (NES). The activation motifs ofTDYand TSH werefound to befully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection ofa multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising ofdifferent amino acids present in MAPK1 and MAPK2 respectively, with respect to rodent and human Plasmodia. 1t is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

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Insights into the Structural Features, Conformational Stability and Functional Activity of the Olneya tesota PF2 Lectin

Protein and Peptide Letters ◽

10.2174/0929866527666200813204303 ◽

2020 ◽

Vol 27 ◽

Author(s):

Edgar Acedo-Espinoza ◽

Irlanda Lagarda-Diaz ◽

Rosina Cabrera ◽

Ana M. Guzman-Partida ◽

Amir Maldonado-Arce ◽

...

Keyword(s):

Tertiary Structure ◽

Proteolytic Enzymes ◽

Conformational Stability ◽

Structural Features ◽

Beta Sheets ◽

Hemagglutinating Activity ◽

Effect Of Temperature ◽

Hydrodynamic Diameter ◽

Bioinformatic Tools ◽

Structural Levels

Background: The O. tesota lectin PF2 is a tetrameric protein with subunits of 33 kDa that recognizes only complex carbohydrates, resistant to proteolytic enzymes and has insecticidal activity against Phaseolus beans pest. Objective: To explore PF2 lectin features at different protein structural levels and to evaluate the effect of temperature and pH on its functionality and conformational stability. Methods: PF2 lectin was purified by affinity chromatography. Its primary structure was resolved by mass spectrometry and analyzed by bioinformatic tools, including its tertiary structure homology modeling. The effect of temperature and pH on its conformational traits and stability was addressed by dynamic light scattering, circular dichroism, and intrinsic fluorescence. The hemagglutinating activity was evaluated using a suspension of peripheral blood erythrocytes. Results: The proposed PF2 folding comprises a high content of beta sheets. At pH 7 and 25 °C, the hydrodynamic diameter (Dh) was found to be 12.3 nm which corresponds to the oligomeric native state of PF2 lectin. Dh increased under the other evaluated pH and temperature conditions, suggesting protein aggregation. At basic pH, PF2 exhibited low conformational stability. The native PF2 (pH 7) retained its full hemagglutinating activity up to 45 °C and exhibited one transition state with a melting temperature of 76.8 °C. Conclusion: PF2 showed distinctive characteristics found in legume lectins. The pH influences the functionality and conformational stability of the protein. PF2 lectin displayed a relatively narrow thermostability to the loss of secondary structure and hemagglutinating activity.

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Closing the gap: an atomistic structural and functional perspective of S. mansoni universal stress G4LZI3 protein in complex with phenolic compounds

Current Drug Discovery Technologies ◽

10.2174/1570163817666201001122436 ◽

2020 ◽

Vol 17 ◽

Author(s):

Priscilla Masamba ◽

Geraldene Munsamy ◽

Abidemi Paul Kappo

Keyword(s):

Phenolic Compounds ◽

Conformational Changes ◽

Stress Protein ◽

Md Simulations ◽

Binding Energies ◽

Developmental Cycle ◽

Structure Based Drug Design ◽

Bioinformatic Tools ◽

Drug Of Choice ◽

Functional Perspective

Background: For decades, Praziquantel has been the undisputed drug of choice for all schistosome infections, but rising concerns due to the unelucidated mechanism of action of the drug and unavoidable reports of emerging drug resistant strains has necessitated the need for alternative treatment drug. Moreover, current apprehension has been reinforced by total dependence on the drug for treatment hence, the search for novel and effective anti-schistosomal drugs. Uses: This study made use of bioinformatic tools to determine the structural binding of the Universal G4LZI3 stress protein (USP) in complex with ten polyphenol compounds, thereby highlighting the effectiveness of these recently identified ‘lead’ molecules in the design of novel therapeutics targeted against schistosomiasis. Upregulation of the G4LZI3 USP throughout the schistosome multifaceted developmental cycle sparks interest in its potential role as a druggable target. The integration of in silico tools provides an atomistic perspective into the binding of potential inhibitors to target proteins. Conclusion: This study therefore, implemented the use of molecular dynamic (MD) simulations to provide functional and structural insight into key conformational changes upon binding of G4ZLI3 to these key phenolic compounds. Post-MD analyses revealed unique structural and conformational changes in the G4LZI3 protein in complex with curcumin and catechin respectively. These systems exhibited the highest binding energies, while the major interacting residues conserved in all the complexes provides a route map for structure-based drug design of novel compounds with enhanced inhibitory potency against the G4LZI3 protein. This study suggests an alternative approach for the development of anti-schistosomal drugs using natural compounds.

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Antigene and Antiproliferative Effects of Triplex-Forming Oligonucleotide (TFO) Targeted on hmgb1 Gene in Human Hepatoma Cells

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520620666200619170438 ◽

2020 ◽

Vol 20 (16) ◽

pp. 1943-1955

Author(s):

Neelam Lohani ◽

Moganty R. Rajeswari

Keyword(s):

Apoptotic Cell ◽

Isothermal Calorimetry ◽

High Mobility ◽

Rational Drug Design ◽

Human Hepatoma Cells ◽

Aberrant Expression ◽

Bioinformatic Tools ◽

Hmgb1 Expression ◽

Dna Triplex ◽

Triplex Forming Oligonucleotide

Background: The high mobility group box 1 (hmgb1) is one of the frequently over-expressed genes whose aberrant expression is reported in a number of human cancers. Various strategies are underway to inhibit hmgb1 expression in cancer cells having considerable therapeutic value. Objective: The present work involves selective transcriptional inhibition of the hmgb1 gene using selective DNA triplex structure-based gene technology. Here, the promoter region of the hmgb1 gene at position (-183 to -165) from the transcription start site as a target was selected using bioinformatic tools. Methods: The DNA triplex formation by the DNA of the target gene and TFO was confirmed using UV absorption spectroscopy, Circular Dichroism, and Isothermal Calorimetry. Results: Treatment of HepG2 cell with specific Triplex-forming Oligonucleotide significantly downregulated HMGB1 expression level at mRNA and protein levels by 50%, while the classical anticancer drugs, actinomycin/ adriamycin as positive controls showed 65% and the combination of TFO and drug decreased by 70%. The anti-proliferative effects of TFO correlated well with the fact of accumulation of cells in the Go phase and apoptotic cell death. Further, the binding of anti-cancer drugs to hmgb1 is stronger in DNA triplex state as compared to hmgb1 alone, suggesting the combination therapy as a better option. Conclusion: Therefore, the ability of hmgb1 targeted triplex-forming oligonucleotide in combination with triplex selective anticancer drug holds promise in the treatment of malignancies associated with hmgb1 overexpression. The result obtained may open up new vistas to provide a basis for the rational drug design and searching for high-affinity ligands with a high triplex selectivity.

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BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

Bioinformatics ◽

10.1093/bioinformatics/btab121 ◽

2021 ◽

Author(s):

Darawan Rinchai ◽

Jessica Roelands ◽

Mohammed Toufiq ◽

Wouter Hendrickx ◽

Matthew C Altman ◽

...

Keyword(s):

Transcript Abundance ◽

R Package ◽

Supplementary Information ◽

Illustrative Case ◽

Bioinformatic Tools ◽

Transcriptional Module ◽

Wide Range ◽

Downstream Analysis ◽

Computing Module ◽

Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

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Intracellular and Extracellular Markers of Lethality in Osteogenesis Imperfecta: A Quantitative Proteomic Approach

International Journal of Molecular Sciences ◽

10.3390/ijms22010429 ◽

2021 ◽

Vol 22 (1) ◽

pp. 429

Author(s):

Luca Bini ◽

Domitille Schvartz ◽

Chiara Carnemolla ◽

Roberta Besio ◽

Nadia Garibaldi ◽

...

Keyword(s):

Osteogenesis Imperfecta ◽

Type I Collagen ◽

Type I ◽

Tandem Mass ◽

Type Ii ◽

Type Iii ◽

Bioinformatic Tools ◽

Proteomic Approach ◽

Fibrillin 1 ◽

Heritable Disorder

Osteogenesis imperfecta (OI) is a heritable disorder that mainly affects the skeleton. The inheritance is mostly autosomal dominant and associated to mutations in one of the two genes, COL1A1 and COL1A2, encoding for the type I collagen α chains. According to more than 1500 described mutation sites and to outcome spanning from very mild cases to perinatal-lethality, OI is characterized by a wide genotype/phenotype heterogeneity. In order to identify common affected molecular-pathways and disease biomarkers in OI probands with different mutations and lethal or surviving phenotypes, primary fibroblasts from dominant OI patients, carrying COL1A1 or COL1A2 defects, were investigated by applying a Tandem Mass Tag labeling-Liquid Chromatography-Tandem Mass Spectrometry (TMT LC-MS/MS) proteomics approach and bioinformatic tools for comparative protein-abundance profiling. While no difference in α1 or α2 abundance was detected among lethal (type II) and not-lethal (type III) OI patients, 17 proteins, with key effects on matrix structure and organization, cell signaling, and cell and tissue development and differentiation, were significantly different between type II and type III OI patients. Among them, some non–collagenous extracellular matrix (ECM) proteins (e.g., decorin and fibrillin-1) and proteins modulating cytoskeleton (e.g., nestin and palladin) directly correlate to the severity of the disease. Their defective presence may define proband-failure in balancing aberrances related to mutant collagen.

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Cascading from SARS-CoV-2 to Parkinson’s Disease through Protein-Protein Interactions

Viruses ◽

10.3390/v13050897 ◽

2021 ◽

Vol 13 (5) ◽

pp. 897

Author(s):

Ernesto Estrada

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Protein Interactions ◽

Molecular Level ◽

Direct Consequence ◽

Viral Proteins ◽

Clinical Findings ◽

Post Translational Modification ◽

Host Proteins ◽

Bioinformatic Tools

Extensive extrapulmonary damages in a dozen of organs/systems, including the central nervous system (CNS), are reported in patients of the coronavirus disease 2019 (COVID-19). Three cases of Parkinson’s disease (PD) have been reported as a direct consequence of COVID-19. In spite of the scarce data for establishing a definitive link between COVID-19 and PD, some hypotheses have been proposed to explain the cases reported. They, however, do not fit well with the clinical findings reported for COVID-19 patients, in general, and for the PD cases reported, in particular. Given the importance of this potential connection, we present here a molecular-level mechanistic hypothesis that explains well these findings and will serve to explore the potential CNS damage in COVID-19 patients. The model explaining the cascade effects from COVID-19 to CNS is developed by using bioinformatic tools. It includes the post-translational modification of host proteins in the lungs by viral proteins, the transport of modified host proteins via exosomes out the lungs, and the disruption of protein-protein interaction in the CNS by these modified host proteins. Our hypothesis is supported by finding 44 proteins significantly expressed in the CNS which are associated with PD and whose interactions can be perturbed by 24 host proteins significantly expressed in the lungs. These 24 perturbators are found to interact with viral proteins and to form part of the cargoes of exosomes in human tissues. The joint set of perturbators and PD-vulnerable proteins form a tightly connected network with significantly more connections than expected by selecting a random cluster of proteins of similar size from the human proteome. The molecular-level mechanistic hypothesis presented here provides several routes for the cascading of effects from the lungs of COVID-19 patients to PD. In particular, the disruption of autophagy/ubiquitination processes appears as an important mechanism that triggers the generation of large amounts of exosomes containing perturbators in their cargo, which would insult several PD-vulnerable proteins, potentially triggering Parkinsonism in COVID-19 patients.

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BioCommons: a robust java library for RNA structural bioinformatics

Bioinformatics ◽

10.1093/bioinformatics/btab069 ◽

2021 ◽

Author(s):

Tomasz Zok

Keyword(s):

Source Code ◽

Structural Bioinformatics ◽

Supplementary Information ◽

Supplementary Data ◽

Bioinformatic Tools ◽

Data Formats ◽

Central Repository ◽

Diverse Data ◽

2D And 3D ◽

Java Library

Abstract Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.

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Bioinformatic tools help molecular characterization of Perkinsus olseni differentially expressed genes

Journal of Integrative Bioinformatics ◽

10.1515/jib-2011-179 ◽

2011 ◽

Vol 8 (3) ◽

pp. 130-140 ◽

Cited By ~ 1

Author(s):

Rita M. T. Ascenso

Keyword(s):

Molecular Characterization ◽

Protozoan Parasite ◽

Bioinformatic Tools ◽

Host Interaction ◽

Ria Formosa ◽

Genes Expression ◽

Bioinformatic Tool ◽

Southern Portugal ◽

Heavy Mortality

Abstract In the 80ies, in Southern Europe and in particular in Ria Formosa there was an episode of heavy mortality of the economically relevant clam Ruditapes (R.) decussatus associated with a debilitating disease (Perkinsosis) caused by Perkinsus olseni. This protozoan parasite was poorly known concerning its’ differential transcriptome in response to its host, R. decussatus. This laboratory available protozoan system was used to identify parasite genes related to host interaction. Beyond the application of molecular biology technologies and methodologies, only the help of Bioinformatics tools allowed to analyze the results of the study. The strategy started with SSH technique, allowing the identification of parasite up-regulated genes in response to its natural host, then a macroarray was constructed and hybridized to characterize the parasite genes expression when exposed to bivalves hemolymph from permissive host (R. decussatus), resistant host (R. philippinarum) and non permissive bivalve (Donax trunculus) that cohabit in the same or adjacent habitats in Southern Portugal. Genes and respective peptides full molecular characterization depended on several Bioinformatic tools application. Also a new Bioinformatic tool was developed.

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